v336

Code changes:

• Added CRAM support for GBIB (#17547). Max
• Added doAssemblyHub.pl script, which should automate the build of an assembly hub from NCBI source files (#13553). Hiram
• Activated new trf v4.09 version for simpleRepeats, simpleRepeat tracks from now on will be using this version (#17580). Hiram
• Added new script bedInvert.pl (#13553). Hiram
• Added support through hg.conf setting for hgGateway survey link with image (#17746). Angie
• Fix for hgTracks links to not force every < a > to POST a form (#17703). Angie
• Fix for hgc that affected clicking into details for large deletion variants (#10937). Angie
• Fix for hgVai to allow for refSeqStatus metadata moving to hgFixed (#17597). Angie
• Fix for hgPublicSessions to no longer cause problems for loaded hubs (#17686, #17659). Jonathan
• Added more configuration options for Mirrors for hgPublicSessions (#17469). Jonathan
• DECIPHER load scripts updated for their new file format (#14465). Jonathan
• Introduced htslib library into kent src. Brian
• Improve hgc list of gene sets in MAF detail page more useful by using long label (#17657). Brian
• Fix for hgTables for alternate CRAM output (#17698). Brian
• Fix DNA alignments on detail page for patches to work if alignment is outside window (#17670). Brian
• Removed the requirement for canDoCoverage hg.conf variable for density display (#17702). Brian
• CIRM: improved error messages and usage statements and file permissions handling. Jim
• CIRM: Change to cdwLib, put in a new call to cutadapt that removed polyA tails slowing BWA calls (#17334). Chris
• CIRM: Change to cdwManiFastqToKallisto, renamed and moved it into the cirm/cdw directory (#16244). Chris
• CIRM: Change to cdwMakeValidFile.c to generate a new variable passing it into the library call for cutadapt (#17334). Chris

Data changes:

• A UniProt track for hg38 (#17717). Max
• Building snp147* tracks for hg19, hg38 (#17209). Angie
• Change refLink to hgFixed.refLink in trackDb (allows for deletion of per-assembly refLink table) (#17713). Brian
• Fixed html errors in genomicSuperDups.html found by hgTablesTest. Galt
• Added important information to the PSL FAQ about protein query coordinates and sizes. Galt
• Minor updates to some HTML links (#17114, #17703). Jonathan